ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

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ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Author
Peter Humburg
Date of publication
None
Maintainer
Peter Humburg <peter.humburg@gmail.com>
License
GPL (>= 2)
Version
1.28.0

View on Bioconductor

Man pages

accessors
Access slots of S4 classes
alignFeature
Read counts relative to annotated features
BindScore
Class "BindScore"
callBindingSites
Predict protein binding sites from high-throughput sequencing...
ChIPseqR-package
Identifying Protein Binding Sites in High-Throughput...
compress-BindScore
Compress BindScore Objects
compress-methods
Methods for Function compress in Package 'ChIPseqR'
compress-ReadCounts
Compress ReadCount Objects
decompress
Extract Read Count and Binding Site Score Representations
decompress-methods
Methods for Function decompress in Package 'ChIPseqR'
exportBindSequence
Export sequence of predicted binding sites
getBindCor
Calculate cross-correlation between read counts
getBindLen
Estimate length of binding and support region
getCutoff
Determine significance threshold for binding site scores
internal
Internal and undocumented functions
pickPeak
Identify peaks above a given threshold
plot-BindScore
Diagnostic Plots for Binding Site Scores
plot-ReadCounts
Diagnostic Plots for Read Counts
plotReads
Plot compact representation of read counts on a chromosome
plotWindow
Plot read counts within a genomic region
pos2gff
Convert genome coordinates into GFF format
ReadCounts
Class "ReadCounts"
RLEBindScore-class
Run-length Encoded Binding Site Scores
RLEReadCounts-class
Run-length Encoded Read Counts
simpleNucCall
Predict nucleosome positions from high-throughput sequencing...
startScore
Score potential protein binding sites
strandPileup
Strand specific read counts
windowCounts
Summarize read counts in a sliding window

Files in this package

ChIPseqR/DESCRIPTION
ChIPseqR/NAMESPACE
ChIPseqR/R
ChIPseqR/R/access.R
ChIPseqR/R/classes.R
ChIPseqR/R/generics.R
ChIPseqR/R/initialize.R
ChIPseqR/R/methods.R
ChIPseqR/R/package.R
ChIPseqR/README.md
ChIPseqR/build
ChIPseqR/build/vignette.rds
ChIPseqR/inst
ChIPseqR/inst/CITATION
ChIPseqR/inst/doc
ChIPseqR/inst/doc/Introduction.R
ChIPseqR/inst/doc/Introduction.Rnw
ChIPseqR/inst/doc/Introduction.pdf
ChIPseqR/man
ChIPseqR/man/BindScore.Rd
ChIPseqR/man/ChIPseqR-package.Rd
ChIPseqR/man/RLEBindScore-class.Rd
ChIPseqR/man/RLEReadCounts-class.Rd
ChIPseqR/man/ReadCounts.Rd
ChIPseqR/man/accessors.Rd
ChIPseqR/man/alignFeature.Rd
ChIPseqR/man/callBindingSites.Rd
ChIPseqR/man/compress-BindScore.Rd
ChIPseqR/man/compress-ReadCounts.Rd
ChIPseqR/man/compress-methods.Rd
ChIPseqR/man/decompress-methods.Rd
ChIPseqR/man/decompress.Rd
ChIPseqR/man/exportBindSequence.Rd
ChIPseqR/man/getBindCor.Rd
ChIPseqR/man/getBindLen.Rd
ChIPseqR/man/getCutoff.Rd
ChIPseqR/man/internal.Rd
ChIPseqR/man/pickPeak.Rd
ChIPseqR/man/plot-BindScore.Rd
ChIPseqR/man/plot-ReadCounts.Rd
ChIPseqR/man/plotReads.Rd
ChIPseqR/man/plotWindow.Rd
ChIPseqR/man/pos2gff.Rd
ChIPseqR/man/simpleNucCall.Rd
ChIPseqR/man/startScore.Rd
ChIPseqR/man/strandPileup.Rd
ChIPseqR/man/windowCounts.Rd
ChIPseqR/src
ChIPseqR/src/include
ChIPseqR/src/include/startScore.h
ChIPseqR/src/startScore.c
ChIPseqR/vignettes
ChIPseqR/vignettes/Introduction.Rnw